Good graphing software: any recommendations?

I need to draw some graphs with error bars and possibly logarithmic scales, maybe even on either axis. Any recommendations? The key thing is that it should be flexible – the task is to show the pattern most of all, so I want to fiddle with the parameters to get the clearest results.

In an ideal world the software would calculate and draw the appropriate error bars based on the input, and produce output in EPS. The minimum is that it runs on Linux (I am not afraid of the configure,make, make install cycle either: in fact I rather miss the days when that was what you had to do for most interesting bits of software.